Police say Tod "Doc" Mishler was taken into custody Thursday, three days after riding across the Outerbridge Crossing linking New Jersey with Staten Island.
A police spokeswoman says he was given a ticket for a desk appearance.
Police say the horses had open sores and were suffering from dehydration and malnutrition.
Animal advocate Christine Whaley leads a group called "Stop Doc Mishler," whose members say Mishler neglects his horses.
His two horses were seized Tuesday for veterinary examinations.
On Monday, Mishler was issued a court summons for blocking traffic and trespassing after he rode one horse and led another across the bridge. He couldn't be reached for comment Thursday.